The recipes REDUCE_SCIENCE_NARROWLINE, REDUCE_SCIENCE_GRADIENT,
REDUCE_SCIENCE_LINEFOREST, and REDUCE_SCIENCE_BROADLINE support the following parameters,
except where noted. Recipe parameters should be supplied in an external file and called by the
command line option -recpars <params.ini>
. For an example recipe-parameter file see Section 6.2.
The parameters are classified for easier identification.
Parameter | Description |
ALIGN_SIDE_BAND | Whether or not to combine sidebands in makecube. |
CLUMP_METHOD | Method for identifying emission clumps: |
CUBE_WCS | The co-ordinate system in which to regrid cubes. |
FINAL_LOWER_VELOCITY | Lower velocity limit for all the cube products. |
FINAL_UPPER_VELOCITY | Upper velocity limit for all the cube products. |
ITERATIONS | Number of iterations. Further iterations refine the identification of emission to exclude from baseline subtraction. One iteration is usually sufficient. |
PIXEL_SCALE | The pixel scale, in arcseconds, of cubes. |
REBIN | Comma-separated list of velocity resolutions to rebin the final spectral cube. The rebinned cubes are in addition to the full-resolution cube. The last can be compressed too (cf. VELOCITY_BIN_FACTOR). |
SPREAD_FWHM_OR_ZERO | Depending on the spreading method, this parameter controls the number of arcseconds at which the envelope of the spreading function goes to zero, or the full-width at half-maximum for the Gaussian envelope. |
SPREAD_METHOD | The method to use when spreading each input pixel between a group of neighbouring output pixels when regridding cubes. |
SPREAD_WIDTH | The number of arcseconds on either side of the output position which receive contributions from the input pixel. |
VELOCITY_BIN_FACTOR | Average contiguous sets of velocity channels by this integer factor, each forming one channel in the reduced output. This compression is intended for the high-resolution ACSIS modes, to save significant storage and processing time, but it also yields better baseline subtraction. |
Parameter | Description |
FRACTION_BAD | The maximum fraction of bad values permitted in a receptor (or receptor’s subband for a hybrid observation) permitted before the a receptor is deemed to be bad. |
RESTRICT_LOWER_VELOCITY | Trims all data to this lower velocity, not just at the end for the products. |
RESTRICT_UPPER_VELOCITY | Trims all data to this upper velocity, not just at the end for the products. |
TRIM_MINIMUM_OVERLAP | The minimum number of desired channels that should overlap after trimming hybrid-mode observations. |
TRIM_PERCENTAGE | The percentage of the total frequency range to trim
from either end. This parameter only takes effect if both
|
TRIM_PERCENTAGE_LOWER | The percentage of the total frequency range to trim from the lower end of the frequency range. |
TRIM_PERCENTAGE_UPPER | The percentage of the total frequency range to trim from the higher end of the frequency range. |
Parameter | Description |
BASELINE_EDGES | Percentage of the full range to fit on either edge of the spectra for baselining purposes. If set to a non-positive value and BASELINE_REGIONS is undefined, then the baseline is derived after smoothing and automatic emission detection. If assigned a negative value, BASELINE_REGIONS, if it is defined, will be used instead to specify where to determine the baseline. |
BASELINE_METHOD | Source of the baseline region. Currently only |
BASELINE_NUMBIN | The number of channels to which the spectral axis is
compressed for automated masking of emission when
BASELINE_METHOD= |
BASELINE_ORDER | The polynomial order to use when baselining cubes. |
BASELINE_REGIONS | A comma-separated list of velocity
ranges each in the format
v1:v2,
from where the baseline should be estimated. It is
countermanded should BASELINE_EDGES be positive.
These can also be used to define where to test baseline
linearity if BASELINE_LINEARITY_LINEWIDTH is
set to |
FREQUENCY_SMOOTH | The number of channels to smooth in the frequency axis when smoothing to determine baselines. This number should be small (∼10) for narrow-line observations and large (∼25) for broad-line observations. |
SPATIAL_SMOOTH | The number of pixels to smooth in both spatial axes when smoothing to determine baselines. |
There are a number of ways to define the baseline regions:
The first two are suitable for broadline emission. The second is desirable in the presence of many lines. The third is the default and most appropriate for a single narrow line.
Parameter | Description |
LV_IMAGE | Permits creation of a longitude-velocity map via primitive _CREATE_LV_IMAGE_ |
LV_AXIS | Specify the axis to collapse in the creation of the longitude-velocity map. |
LV_ESTIMATOR | Specify the collapse statistic in the creation of the longitude-velocity map. |
CREATE_MOMENTS_USING_SNR | If set to true ( |
MOMENTS | Comma separated list of the moments maps to create (integ,iwc). |
MOMENTS_LOWER_VELOCITY | The lower velocity range from which the moments maps will be created. |
MOMENTS_UPPER_VELOCITY | The upper velocity range from which the moments maps will be created. |
Parameter | Description |
FLATFIELD | Whether or not to perform flat-fielding. |
FLAT_APPLY | Whether or not to apply the calculated flatfield. If set false the ratios are still calculated and logged. |
FLAT_METHOD | Flatfield option to ratio voxel by voxel. |
FLAT_LOWER | Sets the lower limit by which to restrict the velocity range where there is astronomical signal for FLAT_METHOD. |
FLAT_UPPER | Sets the upper limit by which to restrict the velocity range where there is astronomical signal for FLAT_METHOD. |
MINSNR | Allow selection of higher signal-to-noise voxels for FLAT_METHOD. |
Parameter | Description |
DESPIKE | Whether or not to perform despiking. |
DESPIKE_BOX | The size, in pixels, of the box used to both find the“background” and for cleaning spikes. |
DESPIKE_CLIP | The clip standard deviations to use when finding spikes in the background-subtracted RMS spectrum. |
DESPIKE_PER_DETECTOR | If a spike is not seen in all detectors, consider setting this
value to |
Parameter | Description |
CHUNKSIZE | Maximum sized chunk used for the group cube. |
CUBE_MAXSIZE | Controls the maximum size of the reduced cube. |
TILE | A true value ( |
Parameter | Description |
HIGHFREQ_INTERFERENCE | If set to true ( |
HIGHFREQ_INTERFERENCE_EDGE_CLIP | Used to reject spectra with high-frequency noise. It is the standard deviation to clip the summed-edginess profile iteratively in order to measure the mean and standard deviation of the profile unaffected by bad spectra. |
HIGHFREQ_INTERFERENCE_THRESH_CLIP | Used to reject spectra with high-frequency noise. This is the number of standard deviations at which to threshold the noise profile above its median level. |
HIGHFREQ_RINGING | Whether or not to test for high-frequency ringing in the spectra. This is where a band of spectra in the time series have the same oscillation frequency and origin with smoothly varying amplitude over time. |
HIGHFREQ_RINGING_MIN_SPECTRA | Minimum number of good spectra for ringing filtering to be attempted (see HIGHFREQ_RINGING). The filter needs to be able to discriminate between the normal unaffected spectra from those with ringing. The value should be at least a few times larger than the number of affected spectra. |
Parameter | Description |
LOWFREQ_INTERFERENCE | If set to true ( |
LOWFREQ_INTERFERENCE_EDGE_CLIP | Used to reject spectra with low-frequency interference. It is the standard deviation to clip the profile of summed-deviations from linearity iteratively in order to measure the mean and standard deviation of the profile unaffected by bad spectra. A comma-separated list will perform iterative sigma clipping of outliers, but standard deviations in the list should not decrease. |
LOWFREQ_INTERFERENCE_MAX_THRESHOLD | Spectra are deemed to be non-linear if their non-linearity exceeds this threshold. |
LOWFREQ_INTERFERENCE_MIN_THRESHOLD | No spectra with non-linearity below this threshold will be rejected. |
LOWFREQ_INTERFERENCE_THRESH_CLIP | Used to reject spectra with low-frequency interference. This is the number of standard deviations at which to threshold the non-linearity profile above its median level. |
BASELINE_LINEARITY
and related parameters below.
These parameters are not available in the REDUCE_SCIENCE_BROADLINE recipe. Parameter | Description |
BASELINE_LINEARITY | If set to true, receptors with mostly or all non-linear baselines are excluded from the reduced products. |
BASELINE_LINEARITY_CLIP | This is used to reject receptors that have non-linear baselines. It is the maximum number of standard deviations above the median RMS deviations for which a detector’s non-linearity is regarded as acceptable. |
BASELINE_LINEARITY_LINEWIDTH | This is used to reject receptors that have non-linear baselines. It is the extent of the source spectral line measured in km s−1, which is excluded from the non-linearity tests. |
BASELINE_LINEARITY_MINRMS | This is used to retain receptors that have noisy or slightly non-linear baselines, or transient bad baselines (cf. LOWFREQ_INTERFERENCE). The parameter is the minimum RMS deviation from linearity, measured in antenna temperature, for a receptor to be flagged as bad. |
BASELINE_LINEARITY_SCALELENGTH | This is used to reject receptors that have non-linear baselines. It is the smoothing scale length in whole pixels. Features narrower than this are filtered out during the background-level determination. It should be should be odd and sufficiently large to remove the noise while not removing the low-frequency patterns in the spectra. |
Parameter | Description |
CALCULATE_STANDARD_ALWAYS | If set true ( |
NOSIDEBANDCORR | If set to |
SIDEBAND | Set the sideband (e.g. |
SIDEBAND_CORR_FACTOR | This allows you to override the sideband-correction factor chosen from the calibration system and provide your own. The data will be multiplied by the value you provide, so you must ensure it is appropriate for the given sideband and LO frequency of your data. The factor should be supplied in floating point. |
Parameter | Description |
SUBTRACT_REF_EMISSION | If true, the recipe will attempt to locate and remove reference (off-position) signal that appears as absorption lines. |
REF_EMISSION_BOXSIZE | The width (in channels) of the largest reference-spectrum line expected, used to find the background before finding spectral lines. If no value is supplied, an iterative approach determines the largest line width. |
REF_EMISSION_COMBINE_DETECTORS | If true, combine all detectors to form the reference spectrum. While it can improve the signal to noise, receptors are strictly viewing slightly different locations and hence each receptor’s reference spectrum will be different. |
REF_EMISSION_COMBINE_REFPOS | Whether to combine observations by their reference
position ( |
REF_EMISSION_MASK_SOURCE | This controls the use of the mask of source emission
already detected for baseline estimation. There are pros
and cons both using the mask ( |
REF_EMISSION_REGIONS | Instead of automated identification of absorption lines, supply a comma-separated list of line extents (v1:v2) in velocity units. These regions are masked and interpolated, the background determined and subtracted from the unmasked representative spectrum to form an approximation to the reference spectrum. |
SUBTRACT_REF_SPECTRUM | If true, the recipe will interpolate across the extents of reference (off-position) lines that you specify, applied to each (reference position or date and/or detector) median spectrum to estimate the respective reference spectrum. |
REF_SPECTRUM_COMBINE_DETECTORS | If true, combine all detectors to form the reference spectrum. While it can improve the signal to noise, receptors are strictly viewing slightly different locations and hence each receptor’s reference spectrum will be different. |
REF_SPECTRUM_COMBINE_REFPOS | Whether to combine observations by their reference
position ( |
REF_SPECTRUM_FILE | An estimated reference spectrum in absorption, with other values set to zero, to remove reference lines that other methods fail to excise |
REF_SPECTRUM_REGIONS | A comma-separated list of line extents (v1:v2) of the locations of absorption lines to excise, measured in velocity units |
Parameter | Description |
STANDING_WAVE | If true ( |
STANDING_WAVE_EMISSION_MASK | If true ( |
STANDING_WAVE_EMISSION_REGIONS | A comma-separated list of velocity ranges, v1:v2, to mask and interpolate across. |
STANDING_WAVE_EMISSION_THRESHOLD | The temperature threshold above which pixels in the
integ map are deemed to have emission. It only applies
if STANDING_WAVE_EMISSION_MASK is true. This
will usually be a small positive value like |
STANDING_WAVE_EMISSION_INTERPOLATE | If true ( |
STANDING_EMISSION_INTERPOLATE_WIDTH | When STANDING_WAVE_EMISSION_INTERPOLATE is true, this is the initial scale length in channels for smooth interpolation. If interpolation is requested, but this parameter is undefined, the initial interpolation scale length is determined empirically. |
STANDING_WAVE_REFINE | If true ( |
STANDING_WAVE_REFINE_METHOD | This decides which source position-position-velocity
(PPV) cube is refined. The default is |
STANDING_WAVE_SMOOTH | If set, a block smooth is applied to the spectra before subtraction. This is normally a single positive odd integer specifying the smoothing kernel width in spectral channels, but there is also a multiscale facility available, if a comma-separated list is assigned to this parameter. |